1
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Olsen JG, Prestel A, Kassem N, Broendum SS, Shamim HM, Simonsen S, Grysbæk M, Mortensen J, Rytkjær LL, Haxholm GW, Marabini R, Holmberg C, Carr AM, Crehuet R, Nielsen O, Kragelund BB. Checkpoint activation by Spd1: a competition-based system relying on tandem disordered PCNA binding motifs. Nucleic Acids Res 2024; 52:2030-2044. [PMID: 38261971 PMCID: PMC10939359 DOI: 10.1093/nar/gkae011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 12/18/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024] Open
Abstract
DNA regulation, replication and repair are processes fundamental to all known organisms and the sliding clamp proliferating cell nuclear antigen (PCNA) is central to all these processes. S-phase delaying protein 1 (Spd1) from S. pombe, an intrinsically disordered protein that causes checkpoint activation by inhibiting the enzyme ribonucleotide reductase, has one of the most divergent PCNA binding motifs known. Using NMR spectroscopy, in vivo assays, X-ray crystallography, calorimetry, and Monte Carlo simulations, an additional PCNA binding motif in Spd1, a PIP-box, is revealed. The two tandemly positioned, low affinity sites exchange rapidly on PCNA exploiting the same binding sites. Increasing or decreasing the binding affinity between Spd1 and PCNA through mutations of either motif compromised the ability of Spd1 to cause checkpoint activation in yeast. These results pinpoint a role for PCNA in Spd1-mediated checkpoint activation and suggest that its tandemly positioned short linear motifs create a neatly balanced competition-based system, involving PCNA, Spd1 and the small ribonucleotide reductase subunit, Suc22R2. Similar mechanisms may be relevant in other PCNA binding ligands where divergent binding motifs so far have gone under the PIP-box radar.
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Affiliation(s)
- Johan G Olsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Noah Kassem
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Sebastian S Broendum
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Hossain Mohammad Shamim
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Signe Simonsen
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Martin Grysbæk
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Josefine Mortensen
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Louise Lund Rytkjær
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Gitte W Haxholm
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Riccardo Marabini
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Christian Holmberg
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Antony M Carr
- Genome Damage and Stability Centre, University of Sussex, John Maynard Smith Building, Falmer, BN1 9RQ, Brighton
| | - Ramon Crehuet
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, c/ Jordi Girona 18-26, 08034 Barcelona
| | - Olaf Nielsen
- Cell cycle and Genome Stability Group, Functional Genomics, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, The Linderstrøm-Lang Centre for Protein Science and REPIN, Department of Biology, Ole Maaloes Vej 5, University of Copenhagen, 2200 Copenhagen N, Denmark
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2
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Dreier JE, Prestel A, Martins JM, Brøndum SS, Nielsen O, Garbers AE, Suga H, Boomsma W, Rogers JM, Hartmann-Petersen R, Kragelund BB. A context-dependent and disordered ubiquitin-binding motif. Cell Mol Life Sci 2022; 79:484. [PMID: 35974206 PMCID: PMC9381478 DOI: 10.1007/s00018-022-04486-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 02/07/2023]
Abstract
Ubiquitin is a small, globular protein that is conjugated to other proteins as a posttranslational event. A palette of small, folded domains recognizes and binds ubiquitin to translate and effectuate this posttranslational signal. Recent computational studies have suggested that protein regions can recognize ubiquitin via a process of folding upon binding. Using peptide binding arrays, bioinformatics, and NMR spectroscopy, we have uncovered a disordered ubiquitin-binding motif that likely remains disordered when bound and thus expands the palette of ubiquitin-binding proteins. We term this motif Disordered Ubiquitin-Binding Motif (DisUBM) and find it to be present in many proteins with known or predicted functions in degradation and transcription. We decompose the determinants of the motif showing it to rely on features of aromatic and negatively charged residues, and less so on distinct sequence positions in line with its disordered nature. We show that the affinity of the motif is low and moldable by the surrounding disordered chain, allowing for an enhanced interaction surface with ubiquitin, whereby the affinity increases ~ tenfold. Further affinity optimization using peptide arrays pushed the affinity into the low micromolar range, but compromised context dependence. Finally, we find that DisUBMs can emerge from unbiased screening of randomized peptide libraries, featuring in de novo cyclic peptides selected to bind ubiquitin chains. We suggest that naturally occurring DisUBMs can recognize ubiquitin as a posttranslational signal to act as affinity enhancers in IDPs that bind to folded and ubiquitylated binding partners.
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Affiliation(s)
- Jesper E Dreier
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.,REPIN, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Andreas Prestel
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - João M Martins
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark
| | - Sebastian S Brøndum
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Olaf Nielsen
- Functional Genomics, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Anna E Garbers
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.,REPIN, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark
| | - Joseph M Rogers
- Department of Drug Design and Pharmacology, University of Copenhagen, Jagtvej 160, 2100, Copenhagen Ø, Denmark
| | - Rasmus Hartmann-Petersen
- REPIN, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark. .,The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark. .,REPIN, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark. .,The Linderstrøm Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.
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3
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CRL4Cdt2 ubiquitin ligase regulates Dna2 and Rad16 (XPF) nucleases by targeting Pxd1 for degradation. PLoS Genet 2020; 16:e1008933. [PMID: 32692737 PMCID: PMC7394458 DOI: 10.1371/journal.pgen.1008933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/31/2020] [Accepted: 06/15/2020] [Indexed: 01/19/2023] Open
Abstract
Structure-specific endonucleases (SSEs) play key roles in DNA replication, recombination, and repair. SSEs must be tightly regulated to ensure genome stability but their regulatory mechanisms remain incompletely understood. Here, we show that in the fission yeast Schizosaccharomyces pombe, the activities of two SSEs, Dna2 and Rad16 (ortholog of human XPF), are temporally controlled during the cell cycle by the CRL4Cdt2 ubiquitin ligase. CRL4Cdt2 targets Pxd1, an inhibitor of Dna2 and an activator of Rad16, for degradation in S phase. The ubiquitination and degradation of Pxd1 is dependent on CRL4Cdt2, PCNA, and a PCNA-binding degron motif on Pxd1. CRL4Cdt2-mediated Pxd1 degradation prevents Pxd1 from interfering with the normal S-phase functions of Dna2. Moreover, Pxd1 degradation leads to a reduction of Rad16 nuclease activity in S phase, and restrains Rad16-mediated single-strand annealing, a hazardous pathway of repairing double-strand breaks. These results demonstrate a new role of the CRL4Cdt2 ubiquitin ligase in genome stability maintenance and shed new light on how SSE activities are regulated during the cell cycle. Structure-specific endonucleases are enzymes that process DNA intermediates generated in DNA replication, recombination, and repair. Proper regulation of these enzymes is critical for maintaining genome stability. Dna2 and XPF are two such enzymes present across eukaryotes, from yeasts to humans. Here, we show that in the fission yeast Schizosaccharomyces pombe, the activities of Dna2 and Rad16 (the equivalent of human XPF) are temporally controlled during the cell cycle by the CRL4Cdt2 ubiquitin E3 ligase. In the S phase of the cell cycle, CRL4Cdt2 promotes the degradation of Pxd1, which is an inhibitor of Dna2 and an activator of Rad16. Through targeting Pxd1 for degradation, CRL4Cdt2 increases the activity of Dna2 in S phase and is important for the normal S-phase function of Dna2. Meanwhile, the degradation of Pxd1 reduces the activity of Rad16 in S phase, and curtails Rad16-dependent single-strand annealing, a mutagenic DNA repair pathway. Our findings uncover a new mechanism regulating two important endonucleases during the cell cycle, and reveal a new way of coordinating endonucleases to safeguard genome stability.
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Zhou X, Curbo S, Zhao Q, Krishnan S, Kuiper R, Karlsson A. Severe mtDNA depletion and dependency on catabolic lipid metabolism in DGUOK knockout mice. Hum Mol Genet 2020; 28:2874-2884. [PMID: 31127938 DOI: 10.1093/hmg/ddz103] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 05/06/2019] [Accepted: 05/13/2019] [Indexed: 12/26/2022] Open
Abstract
Deoxyguanosine kinase (DGUOK) provides guanosine and adenosine nucleotides for mitochondrial DNA (mtDNA) replication, and its deficiency in humans leads to hepatocerebral mtDNA depletion syndrome or to isolated hepatic disease. There are poor treatment options for DGUOK deficiency and the aim of this study was to generate a model for further studies of the disease that could reveal novel treatment strategies. We report a Dguok-deficient mouse strain that, similar to humans, is most severely affected in the liver. The Dguok complete knockout mice (Dguok-/-) were born normal, but began to lose weight at week 6. A change of fur color from black to blueish grey started at week 16 and was complete at week 20. The movements and behavior were indistinguishable compared to wild-type (wt) mice. A decrease of mtDNA copy number occurred in multiple tissues, with the liver being the most severely affected. The mtDNA-encoded protein cytochrome c oxidase was much lower in Dguok-/- liver tissue than in the wt, whereas the expression of the nuclear-encoded succinate dehydrogenase complex subunit A was unaffected. Histopathology showed severe alterations and immunohistochemistry showed signs of both oxidative stress and regeneration in Dguok-/- liver. The subcutaneous fat layer was undetectable in Dguok-/-, which, in addition to gene expression analysis, indicated an altered lipid metabolism. We conclude that Dguok has a major role for the synthesis of deoxyribonucleotides for mtDNA replication particularly in the liver, similar to the human disorder. Our data also show a catabolic lipid metabolism in liver tissue of Dguok-/-.
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Affiliation(s)
- Xiaoshan Zhou
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Sophie Curbo
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Qian Zhao
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Shuba Krishnan
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Raoul Kuiper
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, 141 86 Stockholm, Sweden
| | - Anna Karlsson
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Karolinska University Hospital, 141 86 Stockholm, Sweden
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5
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Prestel A, Wichmann N, Martins JM, Marabini R, Kassem N, Broendum SS, Otterlei M, Nielsen O, Willemoës M, Ploug M, Boomsma W, Kragelund BB. The PCNA interaction motifs revisited: thinking outside the PIP-box. Cell Mol Life Sci 2019; 76:4923-4943. [PMID: 31134302 PMCID: PMC6881253 DOI: 10.1007/s00018-019-03150-0] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Revised: 04/16/2019] [Accepted: 05/13/2019] [Indexed: 02/08/2023]
Abstract
Proliferating cell nuclear antigen (PCNA) is a cellular hub in DNA metabolism and a potential drug target. Its binding partners carry a short linear motif (SLiM) known as the PCNA-interacting protein-box (PIP-box), but sequence-divergent motifs have been reported to bind to the same binding pocket. To investigate how PCNA accommodates motif diversity, we assembled a set of 77 experimentally confirmed PCNA-binding proteins and analyzed features underlying their binding affinity. Combining NMR spectroscopy, affinity measurements and computational analyses, we corroborate that most PCNA-binding motifs reside in intrinsically disordered regions, that structure preformation is unrelated to affinity, and that the sequence-patterns that encode binding affinity extend substantially beyond the boundaries of the PIP-box. Our systematic multidisciplinary approach expands current views on PCNA interactions and reveals that the PIP-box affinity can be modulated over four orders of magnitude by positive charges in the flanking regions. Including the flanking regions as part of the motif is expected to have broad implications, particularly for interpretation of disease-causing mutations and drug-design, targeting DNA-replication and -repair.
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Affiliation(s)
- Andreas Prestel
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Nanna Wichmann
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Joao M Martins
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark
| | - Riccardo Marabini
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Noah Kassem
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Sebastian S Broendum
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Victoria, 3800, Australia
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, Faculty of Medicine and Health Sciences, NTNU Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Olaf Nielsen
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Martin Willemoës
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Michael Ploug
- Finsen Laboratory, Rigshospitalet, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
- Finsen Laboratory, Biotechnology Research Innovation Centre, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark
| | - Wouter Boomsma
- Department of Computer Science, University of Copenhagen, Universitetsparken 1, 2100, Copenhagen Ø, Denmark.
| | - Birthe B Kragelund
- Department of Biology, University of Copenhagen, Ole Maaloes Vej 5, 2200, Copenhagen N, Denmark.
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6
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Pai CC, Hsu KF, Durley SC, Keszthelyi A, Kearsey SE, Rallis C, Folkes LK, Deegan R, Wilkins SE, Pfister SX, De León N, Schofield CJ, Bähler J, Carr AM, Humphrey TC. An essential role for dNTP homeostasis following CDK-induced replication stress. J Cell Sci 2019; 132:jcs226969. [PMID: 30674555 PMCID: PMC6451416 DOI: 10.1242/jcs.226969] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Accepted: 01/02/2019] [Indexed: 02/03/2023] Open
Abstract
Replication stress is a common feature of cancer cells, and thus a potentially important therapeutic target. Here, we show that cyclin-dependent kinase (CDK)-induced replication stress, resulting from Wee1 inactivation, is synthetic lethal with mutations disrupting dNTP homeostasis in fission yeast. Wee1 inactivation leads to increased dNTP demand and replication stress through CDK-induced firing of dormant replication origins. Subsequent dNTP depletion leads to inefficient DNA replication, DNA damage and to genome instability. Cells respond to this replication stress by increasing dNTP supply through histone methyltransferase Set2-dependent MBF-induced expression of Cdc22, the catalytic subunit of ribonucleotide reductase (RNR). Disrupting dNTP synthesis following Wee1 inactivation, through abrogating Set2-dependent H3K36 tri-methylation or DNA integrity checkpoint inactivation results in critically low dNTP levels, replication collapse and cell death, which can be rescued by increasing dNTP levels. These findings support a 'dNTP supply and demand' model in which maintaining dNTP homeostasis is essential to prevent replication catastrophe in response to CDK-induced replication stress.
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Affiliation(s)
- Chen-Chun Pai
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Kuo-Feng Hsu
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
- Department of Surgery, Tri-Service General Hospital, National Defense Medical Centre, Taipei 114, Taiwan
| | - Samuel C Durley
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Andrea Keszthelyi
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, Sussex, BN1 9RQ, UK
| | - Stephen E Kearsey
- Department of Zoology, University of Oxford, Zoology Research & Administration Building, Mansfield Road, Oxford, OX1 3PS, UK
| | - Charalampos Rallis
- Research Department of Genetics, Evolution & Environment, University College London, London, WC1E 6BT, UK
- School of Health, Sport and Bioscience, University of East London, Stratford Campus, E15 4LZ, London, UK
| | - Lisa K Folkes
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Rachel Deegan
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Sarah E Wilkins
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Sophia X Pfister
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford, OX3 7DQ, UK
| | - Nagore De León
- Department of Zoology, University of Oxford, Zoology Research & Administration Building, Mansfield Road, Oxford, OX1 3PS, UK
| | - Christopher J Schofield
- Chemistry Research Laboratory, Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Jürg Bähler
- Research Department of Genetics, Evolution & Environment, University College London, London, WC1E 6BT, UK
| | - Antony M Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, Sussex, BN1 9RQ, UK
| | - Timothy C Humphrey
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford, OX3 7DQ, UK
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7
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Single-molecule analysis reveals that DNA replication dynamics vary across the course of schizogony in the malaria parasite Plasmodium falciparum. Sci Rep 2017. [PMID: 28638076 PMCID: PMC5479783 DOI: 10.1038/s41598-017-04407-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The mechanics of DNA replication and cell cycling are well-characterized in model organisms, but less is known about these basic aspects of cell biology in early-diverging Apicomplexan parasites, which do not divide by canonical binary fission but undergo unconventional cycles. Schizogony in the malaria parasite, Plasmodium, generates ~16–24 new nuclei via independent, asynchronous rounds of genome replication prior to cytokinesis and little is known about the control of DNA replication that facilitates this. We have characterised replication dynamics in P. falciparum throughout schizogony, using DNA fibre labelling and combing to visualise replication forks at a single-molecule level. We show that origins are very closely spaced in Plasmodium compared to most model systems, and that replication dynamics vary across the course of schizogony, from faster synthesis rates and more widely-spaced origins through to slower synthesis rates and closer-spaced origins. This is the opposite of the pattern usually seen across S-phase in human cells, when a single genome is replicated. Replication forks also appear to stall at an unusually high rate throughout schizogony. Our work explores Plasmodium DNA replication in unprecedented detail and opens up tremendous scope for analysing cell cycle dynamics and developing interventions targetting this unique aspect of malaria biology.
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8
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Fleck O, Fahnøe U, Løvschal KV, Gasasira MFU, Marinova IN, Kragelund BB, Carr AM, Hartsuiker E, Holmberg C, Nielsen O. Deoxynucleoside Salvage in Fission Yeast Allows Rescue of Ribonucleotide Reductase Deficiency but Not Spd1-Mediated Inhibition of Replication. Genes (Basel) 2017; 8:E128. [PMID: 28441348 PMCID: PMC5448002 DOI: 10.3390/genes8050128] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 04/10/2017] [Accepted: 04/20/2017] [Indexed: 12/12/2022] Open
Abstract
In fission yeast, the small, intrinsically disordered protein S-phase delaying protein 1 (Spd1) blocks DNA replication and causes checkpoint activation at least in part, by inhibiting the enzyme ribonucleotide reductase, which is responsible for the synthesis of DNA. The CRL4Cdt2 E3 ubiquitin ligase mediates degradation of Spd1 and the related protein Spd2 at S phase of the cell cycle. We have generated a conditional allele of CRL4Cdt2, by expressing the highly unstable substrate-recruiting protein Cdt2 from a repressible promoter. Unlike Spd1, Spd2 does not regulate deoxynucleotide triphosphate (dNTP) pools; yet we find that Spd1 and Spd2 together inhibit DNA replication upon Cdt2 depletion. To directly test whether this block of replication was solely due to insufficient dNTP levels, we established a deoxy-nucleotide salvage pathway in fission yeast by expressing the human nucleoside transporter human equilibrative nucleoside transporter 1 (hENT1) and the Drosophila deoxynucleoside kinase. We present evidence that this salvage pathway is functional, as 2 µM of deoxynucleosides in the culture medium is able to rescue the growth of two different temperature-sensitive alleles controlling ribonucleotide reductase. However, salvage completely failed to rescue S phase delay, checkpoint activation, and damage sensitivity, which was caused by CRL4Cdt2 inactivation, suggesting that Spd1-in addition to repressing dNTP synthesis-together with Spd2, can inhibit other replication functions. We propose that this inhibition works at the point of the replication clamp proliferating cell nuclear antigen, a co-factor for DNA replication.
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Affiliation(s)
- Oliver Fleck
- Cell Cycle and Genome Stability Group, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
- North West Cancer Research Institute, Bangor University, Bangor, Gwynedd LL57 2UW, UK.
| | - Ulrik Fahnøe
- Cell Cycle and Genome Stability Group, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Katrine Vyff Løvschal
- Cell Cycle and Genome Stability Group, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | | | - Irina N Marinova
- Cell Cycle and Genome Stability Group, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Birthe B Kragelund
- Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Antony M Carr
- Genome Damage and Stability Centre, University of Sussex, Brighton BN1 9RQ, UK.
| | - Edgar Hartsuiker
- North West Cancer Research Institute, Bangor University, Bangor, Gwynedd LL57 2UW, UK.
| | - Christian Holmberg
- Cell Cycle and Genome Stability Group, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
| | - Olaf Nielsen
- Cell Cycle and Genome Stability Group, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.
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9
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Hollenbaugh JA, Shelton J, Tao S, Amiralaei S, Liu P, Lu X, Goetze RW, Zhou L, Nettles JH, Schinazi RF, Kim B. Substrates and Inhibitors of SAMHD1. PLoS One 2017; 12:e0169052. [PMID: 28046007 PMCID: PMC5207538 DOI: 10.1371/journal.pone.0169052] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/09/2016] [Indexed: 11/19/2022] Open
Abstract
SAMHD1 hydrolyzes 2'-deoxynucleoside-5'-triphosphates (dNTPs) into 2'-deoxynucleosides and inorganic triphosphate products. In this paper, we evaluated the impact of 2' sugar moiety substitution for different nucleotides on being substrates for SAMHD1 and mechanisms of actions for the results. We found that dNTPs ((2'R)-2'-H) are only permissive in the catalytic site of SAMHD1 due to L150 exclusion of (2'R)-2'-F and (2'R)-2'-OH nucleotides. However, arabinose ((2'S)-2'-OH) nucleoside-5'-triphosphates analogs are permissive to bind in the catalytic site and be hydrolyzed by SAMHD1. Moreover, when the (2'S)-2' sugar moiety is increased to a (2'S)-2'-methyl as with the SMDU-TP analog, we detect inhibition of SAMHD1’s dNTPase activity. Our computational modeling suggests that (2'S)-2'-methyl sugar moiety clashing with the Y374 of SAMHD1. We speculate that SMDU-TP mechanism of action requires that the analog first docks in the catalytic pocket of SAMHD1 but prevents the A351-V378 helix conformational change from being completed, which is needed before hydrolysis can occur. Collectively we have identified stereoselective 2' substitutions that reveal nucleotide substrate specificity for SAMHD1, and a novel inhibitory mechanism for the dNTPase activity of SAMHD1. Importantly, our data is beneficial for understanding if FDA-approved antiviral and anticancer nucleosides are hydrolyzed by SAMHD1 in vivo.
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Affiliation(s)
- Joseph A. Hollenbaugh
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Jadd Shelton
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Sijia Tao
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Sheida Amiralaei
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Peng Liu
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Xiao Lu
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Russell W. Goetze
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Longhu Zhou
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - James H. Nettles
- Department of Biomedical Informatics and Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Raymond F. Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
| | - Baek Kim
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia United States of America
- Children’s Healthcare of Atlanta, Atlanta, Georgia United States of America
- College of Pharmacy, Kyung-Hee University, Seoul, South Korea
- * E-mail:
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10
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Abstract
Cancer was recognized as a genetic disease at least four decades ago, with the realization that the spontaneous mutation rate must increase early in tumorigenesis to account for the many mutations in tumour cells compared with their progenitor pre-malignant cells. Abnormalities in the deoxyribonucleotide pool have long been recognized as determinants of DNA replication fidelity, and hence may contribute to mutagenic processes that are involved in carcinogenesis. In addition, many anticancer agents antagonize deoxyribonucleotide metabolism. Here, we consider the extent to which aspects of deoxyribonucleotide metabolism contribute to our understanding of both carcinogenesis and to the effective use of anticancer agents.
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Affiliation(s)
- Christopher K Mathews
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon 97331-7305, USA
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11
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Skoneczna A, Kaniak A, Skoneczny M. Genetic instability in budding and fission yeast-sources and mechanisms. FEMS Microbiol Rev 2015; 39:917-67. [PMID: 26109598 PMCID: PMC4608483 DOI: 10.1093/femsre/fuv028] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/26/2015] [Indexed: 12/17/2022] Open
Abstract
Cells are constantly confronted with endogenous and exogenous factors that affect their genomes. Eons of evolution have allowed the cellular mechanisms responsible for preserving the genome to adjust for achieving contradictory objectives: to maintain the genome unchanged and to acquire mutations that allow adaptation to environmental changes. One evolutionary mechanism that has been refined for survival is genetic variation. In this review, we describe the mechanisms responsible for two biological processes: genome maintenance and mutation tolerance involved in generations of genetic variations in mitotic cells of both Saccharomyces cerevisiae and Schizosaccharomyces pombe. These processes encompass mechanisms that ensure the fidelity of replication, DNA lesion sensing and DNA damage response pathways, as well as mechanisms that ensure precision in chromosome segregation during cell division. We discuss various factors that may influence genome stability, such as cellular ploidy, the phase of the cell cycle, transcriptional activity of a particular region of DNA, the proficiency of DNA quality control systems, the metabolic stage of the cell and its respiratory potential, and finally potential exposure to endogenous or environmental stress. The stability of budding and fission yeast genomes is influenced by two contradictory factors: (1) the need to be fully functional, which is ensured through the replication fidelity pathways of nuclear and mitochondrial genomes through sensing and repairing DNA damage, through precise chromosome segregation during cell division; and (2) the need to acquire changes for adaptation to environmental challenges.
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Affiliation(s)
- Adrianna Skoneczna
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Aneta Kaniak
- Laboratory of Mutagenesis and DNA Repair, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
| | - Marek Skoneczny
- Department of Genetics, Institute of Biochemistry and Biophysics, Polish Academy of Science, 02-106 Warsaw, Poland
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12
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Meurisse J, Bacquin A, Richet N, Charbonnier JB, Ochsenbein F, Peyroche A. Hug1 is an intrinsically disordered protein that inhibits ribonucleotide reductase activity by directly binding Rnr2 subunit. Nucleic Acids Res 2014; 42:13174-85. [PMID: 25378334 PMCID: PMC4245953 DOI: 10.1093/nar/gku1095] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Rad53 is a conserved protein kinase with a central role in DNA damage response and nucleotide metabolism. We observed that the expression of a dominant-lethal form of RAD53 leads to significant expression changes for at least 16 genes, including the RNR3 and the HUG1 genes, both of which are involved in the control of nucleotide metabolism. We established by multiple biophysical and biochemical approaches that Hug1 is an intrinsically disordered protein that directly binds to the small RNR subunit Rnr2. We characterized the surface of interaction involved in Hug1 binding to Rnr2, and we thus defined a new binding region to Rnr2. Moreover, we show that Hug1 is deleterious to cell growth in the context of reduced RNR activity. This inhibitory effect of Hug1 on RNR activity depends on the binding of Hug1 to Rnr2. We propose a model in which Hug1 modulates Rnr2-Rnr1 association by binding Rnr2. We show that Hug1 accumulates under various physiological conditions of high RNR induction. Hence, both the regulation and the mode of action of Hug1 are different from those of the small protein inhibitors Dif1 and Sml1, and Hug1 can be considered as a regulator for fine-tuning of RNR activity.
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Affiliation(s)
- Julie Meurisse
- CEA, iBiTecS, SBIGeM, Gif-sur-Yvette, F-91191, France CNRS-Université Paris Sud, FRE 3377, Gif-sur-Yvette, F-91191, France
| | - Agathe Bacquin
- CEA, iBiTecS, SBIGeM, Gif-sur-Yvette, F-91191, France CNRS-Université Paris Sud, FRE 3377, Gif-sur-Yvette, F-91191, France
| | - Nicolas Richet
- CEA, iBiTecS, SBSM, Laboratoire de Biologie Structurale et Radiobiologie, Gif-sur-Yvette, F-91191, France CNRS, UMR8221, Gif-sur-Yvette, F-91191, France
| | - Jean-Baptiste Charbonnier
- CEA, iBiTecS, SBSM, Laboratoire de Biologie Structurale et Radiobiologie, Gif-sur-Yvette, F-91191, France CNRS, UMR8221, Gif-sur-Yvette, F-91191, France
| | - Françoise Ochsenbein
- CEA, iBiTecS, SBSM, Laboratoire de Biologie Structurale et Radiobiologie, Gif-sur-Yvette, F-91191, France CNRS, UMR8221, Gif-sur-Yvette, F-91191, France
| | - Anne Peyroche
- CEA, iBiTecS, SBIGeM, Gif-sur-Yvette, F-91191, France CNRS-Université Paris Sud, FRE 3377, Gif-sur-Yvette, F-91191, France
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13
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Slenn TJ, Morris B, Havens CG, Freeman RM, Takahashi TS, Walter JC. Thymine DNA glycosylase is a CRL4Cdt2 substrate. J Biol Chem 2014; 289:23043-23055. [PMID: 24947512 DOI: 10.1074/jbc.m114.574194] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The E3 ubiquitin ligase CRL4(Cdt2) targets proteins for destruction in S phase and after DNA damage by coupling ubiquitylation to DNA-bound proliferating cell nuclear antigen (PCNA). Coupling to PCNA involves a PCNA-interacting peptide (PIP) degron motif in the substrate that recruits CRL4(Cdt2) while binding to PCNA. In vertebrates, CRL4(Cdt2) promotes degradation of proteins whose presence in S phase is deleterious, including Cdt1, Set8, and p21. Here, we show that CRL4(Cdt2) targets thymine DNA glycosylase (TDG), a base excision repair enzyme that is involved in DNA demethylation. TDG contains a conserved and nearly perfect match to the PIP degron consensus. TDG is ubiquitylated and destroyed in a PCNA-, Cdt2-, and PIP degron-dependent manner during DNA repair in Xenopus egg extract. The protein can also be destroyed during DNA replication in this system. During Xenopus development, TDG first accumulates during gastrulation, and its expression is down-regulated by CRL4(Cdt2). Our results expand the group of vertebrate CRL4(Cdt2) substrates to include a bona fide DNA repair enzyme.
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Affiliation(s)
- Tamara J Slenn
- Departments of Biological Chemistry and Molecular Pharmacology and Harvard Medical School, Boston, Massachusetts 02115
| | - Benjamin Morris
- Departments of Biological Chemistry and Molecular Pharmacology and Harvard Medical School, Boston, Massachusetts 02115
| | - Courtney G Havens
- Departments of Biological Chemistry and Molecular Pharmacology and Harvard Medical School, Boston, Massachusetts 02115
| | - Robert M Freeman
- Departments of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115
| | | | - Johannes C Walter
- Departments of Biological Chemistry and Molecular Pharmacology and Harvard Medical School, Boston, Massachusetts 02115; Howard Hughes Medical Institute, Harvard University, Boston, Massachusetts 02115.
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14
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Vejrup-Hansen R, Fleck O, Landvad K, Fahnøe U, Broendum SS, Schreurs AS, Kragelund BB, Carr AM, Holmberg C, Nielsen O. Spd2 assists Spd1 in the modulation of ribonucleotide reductase architecture but does not regulate deoxynucleotide pools. J Cell Sci 2014; 127:2460-70. [PMID: 24652833 DOI: 10.1242/jcs.139816] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024] Open
Abstract
In yeasts, small intrinsically disordered proteins (IDPs) modulate ribonucleotide reductase (RNR) activity to ensure an optimal supply of dNTPs for DNA synthesis. The Schizosaccharomyces pombe Spd1 protein can directly inhibit the large RNR subunit (R1), import the small subunit (R2) into the nucleus and induce an architectural change in the R1-R2 holocomplex. Here, we report the characterization of Spd2, a protein with sequence similarity to Spd1. We show that Spd2 is a CRL4(Cdt2)-controlled IDP that functions together with Spd1 in the DNA damage response and in modulation of RNR architecture. However, Spd2 does not regulate dNTP pools and R2 nuclear import. Furthermore, deletion of spd2 only weakly suppresses the Rad3(ATR) checkpoint dependency of CRL4(Cdt2) mutants. However, when we raised intracellular dNTP pools by inactivation of RNR feedback inhibition, deletion of spd2 could suppress the checkpoint dependency of CRL4(Cdt2) mutant cells to the same extent as deletion of spd1. Collectively, these observations suggest that Spd1 on its own regulates dNTP pools, whereas in combination with Spd2 it modulates RNR architecture and sensitizes cells to DNA damage.
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Affiliation(s)
- Rasmus Vejrup-Hansen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N., Denmark
| | - Oliver Fleck
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N., Denmark NWCR Institute, School of Biological Sciences, Bangor University, Bangor, Gwynedd, LL57 2UW, UK
| | - Katrine Landvad
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N., Denmark
| | - Ulrik Fahnøe
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N., Denmark
| | - Sebastian S Broendum
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N., Denmark
| | - Ann-Sofie Schreurs
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
| | - Birthe B Kragelund
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N., Denmark
| | - Antony M Carr
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, East Sussex BN1 9RQ, UK
| | - Christian Holmberg
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N., Denmark
| | - Olaf Nielsen
- Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N., Denmark
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15
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Guarino E, Salguero I, Kearsey SE. Cellular regulation of ribonucleotide reductase in eukaryotes. Semin Cell Dev Biol 2014; 30:97-103. [PMID: 24704278 DOI: 10.1016/j.semcdb.2014.03.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2013] [Accepted: 03/26/2014] [Indexed: 12/22/2022]
Abstract
Synthesis of deoxynucleoside triphosphates (dNTPs) is essential for both DNA replication and repair and a key step in this process is catalyzed by ribonucleotide reductases (RNRs), which reduce ribonucleotides (rNDPs) to their deoxy forms. Tight regulation of RNR is crucial for maintaining the correct levels of all four dNTPs, which is important for minimizing the mutation rate and avoiding genome instability. Although allosteric control of RNR was the first discovered mechanism involved in regulation of the enzyme, other controls have emerged in recent years. These include regulation of expression of RNR genes, proteolysis of RNR subunits, control of the cellular localization of the small RNR subunit, and regulation of RNR activity by small protein inhibitors. This review will focus on these additional mechanisms of control responsible for providing a balanced supply of dNTPs.
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Affiliation(s)
- Estrella Guarino
- Tinbergen Building, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom.
| | - Israel Salguero
- Tinbergen Building, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom.
| | - Stephen E Kearsey
- Tinbergen Building, Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, United Kingdom.
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16
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Shao J, Liu X, Zhu L, Yen Y. Targeting ribonucleotide reductase for cancer therapy. Expert Opin Ther Targets 2013; 17:1423-37. [PMID: 24083455 DOI: 10.1517/14728222.2013.840293] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Ribonucleotide reductase (RR) is a unique enzyme, because it is responsible for reducing ribonucleotides to their corresponding deoxyribonucleotides, which are the building blocks required for DNA replication and repair. Dysregulated RR activity is associated with genomic instability, malignant transformation and cancer development. The use of RR inhibitors, either as a single agent or combined with other therapies, has proven to be a promising approach for treating solid tumors and hematological malignancies. AREAS COVERED This review covers recent publications in the area of RR, which include: i) the structure, function and regulation of RR; ii) the roles of RR in cancer development; iii) the classification, mechanisms and clinical application of RR inhibitors for cancer therapy and iv) strategies for developing novel RR inhibitors in the future. EXPERT OPINION Exploring the possible nonenzymatic roles of RR subunit proteins in carcinogenesis may lead to new rationales for developing novel anticancer drugs. Updated information about the structure and holoenzyme models of RR will help in identifying potential sites in the protein that could be targets for novel RR inhibitors. Determining RR activity and subunit levels in clinical samples will provide a rational platform for developing personalized cancer therapies that use RR inhibitors.
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Affiliation(s)
- Jimin Shao
- Zhejiang University, School of Medicine, Department of Pathology and Pathophysiology , Hangzhou 310058 , China
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17
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Fleck O, Vejrup-Hansen R, Watson A, Carr AM, Nielsen O, Holmberg C. Spd1 accumulation causes genome instability independently of ribonucleotide reductase activity but functions to protect the genome when deoxynucleotide pools are elevated. J Cell Sci 2013; 126:4985-94. [PMID: 23986475 DOI: 10.1242/jcs.132837] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Cullin4, Ddb1 and Cdt2 are core subunits of the ubiquitin ligase complex CRL4(Cdt2), which controls genome stability by targeting Spd1 for degradation during DNA replication and repair in fission yeast. Spd1 has an inhibitory effect on ribonucleotide reductase (RNR), the activity of which is required for deoxynucleotide (dNTP) synthesis. The failure to degrade Spd1 in mutants where CRL4(Cdt2) is defective leads to DNA integrity checkpoint activation and dependency. This correlates with a lower dNTP pool. Pools are restored in a spd1-deleted background and this also suppresses checkpoint activation and dependency. We hypothesized that fission yeast with RNR hyperactivity would display a mutator phenotype on their own, but also possibly repress aspects of the phenotype associated with the inability to target Spd1 for degradation. Here, we report that a mutation in the R1 subunit of ribonucleotide reductase cdc22 (cdc22-D57N), which alleviated allosteric feedback inhibition, caused a highly elevated dNTP pool that was further increased by deleting spd1. The Δspd1 cdc22-D57N double mutant had elevated mutation rates and was sensitive to damaging agents that cause DNA strand breaks, demonstrating that Spd1 can protect the genome when dNTP pools are high. In ddb1-deleted cells, cdc22-D57N also potently elevated RNR activity, but failed to allow cell growth independently of the intact checkpoint. Our results provide evidence that excess Spd1 interferes with other functions in addition to its inhibitory effect on ribonucleotide reduction to generate replication stress and genome instability.
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Affiliation(s)
- Oliver Fleck
- Cell Cycle and Genome Stability Group, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, 2200 Copenhagen N, Denmark
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18
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Hollenbaugh JA, Gee P, Baker J, Daly MB, Amie SM, Tate J, Kasai N, Kanemura Y, Kim DH, Ward BM, Koyanagi Y, Kim B. Host factor SAMHD1 restricts DNA viruses in non-dividing myeloid cells. PLoS Pathog 2013; 9:e1003481. [PMID: 23825958 PMCID: PMC3694861 DOI: 10.1371/journal.ppat.1003481] [Citation(s) in RCA: 133] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 05/22/2013] [Indexed: 01/01/2023] Open
Abstract
SAMHD1 is a newly identified anti-HIV host factor that has a dNTP triphosphohydrolase activity and depletes intracellular dNTP pools in non-dividing myeloid cells. Since DNA viruses utilize cellular dNTPs, we investigated whether SAMHD1 limits the replication of DNA viruses in non-dividing myeloid target cells. Indeed, two double stranded DNA viruses, vaccinia and herpes simplex virus type 1, are subject to SAMHD1 restriction in non-dividing target cells in a dNTP dependent manner. Using a thymidine kinase deficient strain of vaccinia virus, we demonstrate a greater restriction of viral replication in non-dividing cells expressing SAMHD1. Therefore, this study suggests that SAMHD1 is a potential innate anti-viral player that suppresses the replication of a wide range of DNA viruses, as well as retroviruses, which infect non-dividing myeloid cells. Various viral pathogens such as HIV-1, herpes simplex virus (HSV) and vaccinia virus infect terminally-differentiated/non-dividing macrophages during the course of viral pathogenesis. Unlike dividing cells, non-dividing cells lack chromosomal DNA replication, do not enter the cell cycle, and harbor very low levels of cellular dNTPs, which are substrates of viral DNA polymerases. A series of recent studies revealed that the host protein SAMHD1 is dNTP triphosphohydrolase, which contributes to the poor dNTP abundance in non-dividing myeloid cells, and restricts proviral DNA synthesis of HIV-1 and other lentiviruses in macrophages, dendritic cells, and resting T cells. In this report, we demonstrate that SAMHD1 also controls the replication of large dsDNA viruses: vaccinia virus and HSV-1, in primary human monocyte-derived macrophages. SAMHD1 suppresses the replication of these DNA viruses to an even greater extent in the absence of viral genes that are involved in dNTP metabolism such as thymidine kinase. Therefore, this study supports that dsDNA viruses evolved to express enzymes necessary to increase the levels of dNTPs as a mechanism to overcome the restriction induced by SAMHD1 in myeloid cells.
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Affiliation(s)
- Joseph A. Hollenbaugh
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
- Center for Drug Discovery, The Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Peter Gee
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Jonathon Baker
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - Michele B. Daly
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
- Center for Drug Discovery, The Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
| | - Sarah M. Amie
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - Jessica Tate
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
| | - Natsumi Kasai
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Yuka Kanemura
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Dong-Hyun Kim
- Department of Pharmacy, Kyung-Hee University, Seoul, South Korea
| | - Brian M. Ward
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
- * E-mail: (BW); (YK); (BK)
| | - Yoshio Koyanagi
- Laboratory of Viral Pathogenesis, Institute for Virus Research, Kyoto University, Kyoto, Japan
- * E-mail: (BW); (YK); (BK)
| | - Baek Kim
- Department of Microbiology and Immunology, University of Rochester, Rochester, New York, United States of America
- Center for Drug Discovery, The Department of Pediatrics, Emory University, Atlanta, Georgia, United States of America
- Department of Pharmacy, Kyung-Hee University, Seoul, South Korea
- * E-mail: (BW); (YK); (BK)
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19
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Cameron RS, Liu C, Pihkala JPS. Myosin 16 levels fluctuate during the cell cycle and are downregulated in response to DNA replication stress. Cytoskeleton (Hoboken) 2013; 70:328-48. [PMID: 23596177 DOI: 10.1002/cm.21109] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Accepted: 03/27/2013] [Indexed: 01/03/2023]
Abstract
Myosins comprise a highly conserved superfamily of eukaryotic actin-dependent motor proteins implicated in a large repertoire of functions in both the cytoplasm and the nucleus. Class XVI myosin, MYO16, reveals expression in most somatic as well as meiotic cells with prominent localization in the nucleus, excepting the nucleolus; however, the role(s) of Myo16 in the nucleus remain unknown. In this report, we investigated Myo16 abundance during transit through the cell cycle. Immunolocalization, immunoblot, flow cytometric and quantitative RT-PCR studies performed in Rat2 cells indicate that Myo16 mRNA and protein abundance are cell cycle regulated: in the unperturbed cell cycle, each rises to peak levels in late G1 and thereon through S-phase and each decays as cells enter M-phase. Notably, RNA interference-induced Myo16 depletion results in altered cell cycle distribution as well as in large-scale cell death. In response to DNA replication stress (impaired replication fork progression as a consequence of DNA damage, lack of sufficient deoxynucleotides, or inhibition of DNA polymerases), Myo16 protein shows substantial loss. Attenuation of replication stress (aphidicolin or hydroxyurea) is followed by a recovery of Myo16 expression and resumption of S-phase progression. Collectively, these observations suggest that Myo16 may play a regulatory role in cell cycle progression.
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Affiliation(s)
- Richard S Cameron
- Institute of Molecular Medicine and Genetics, Department of Medicine, Georgia Regents University, Medical College of Georgia, Augusta, Georgia 30912, USA.
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20
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Hua H, Namdar M, Ganier O, Gregan J, Méchali M, Kearsey SE. Sequential steps in DNA replication are inhibited to ensure reduction of ploidy in meiosis. Mol Biol Cell 2013; 24:578-87. [PMID: 23303250 PMCID: PMC3583662 DOI: 10.1091/mbc.e12-11-0825] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Reduction in ploidy in meiosis is assumed to be due to a block to the licensing step (Mcm helicase association with replication origins). When the licensing block is subverted, replication is still only partial due to inefficient elongation replication forks. This might constitute an additional level of replication regulation. Meiosis involves two successive rounds of chromosome segregation without an intervening S phase. Exit from meiosis I is distinct from mitotic exit, in that replication origins are not licensed by Mcm2-7 chromatin binding, but spindle disassembly occurs during a transient interphase-like state before meiosis II. The absence of licensing is assumed to explain the block to DNA replication, but this has not been formally tested. Here we attempt to subvert this block by expressing the licensing control factors Cdc18 and Cdt1 during the interval between meiotic nuclear divisions. Surprisingly, this leads only to a partial round of DNA replication, even when these factors are overexpressed and effect clear Mcm2-7 chromatin binding. Combining Cdc18 and Cdt1 expression with modulation of cyclin-dependent kinase activity, activation of Dbf4-dependent kinase, or deletion of the Spd1 inhibitor of ribonucleotide reductase has little additional effect on the extent of DNA replication. Single-molecule analysis indicates this partial round of replication results from inefficient progression of replication forks, and thus both initiation and elongation replication steps may be inhibited in late meiosis. In addition, DNA replication or damage during the meiosis I–II interval fails to arrest meiotic progress, suggesting absence of checkpoint regulation of meiosis II entry.
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Affiliation(s)
- Hui Hua
- Department of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom
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21
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Abstract
Correct regulation of DNA nucleotide biosynthesis is emerging as a key issue of importance for genome integrity. The fission yeast Spd1 protein can modulate the activity of ribonucleotide reductase (RNR) by at least three different mechanisms. Now a paper reports that Spd1 turnover is linked to ongoing DNA synthesis.
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Affiliation(s)
- Christian Holmberg
- Cell cycle and Genome Stability Group, Department of Biology, University of Copenhagen, Ole Maaløes vej 5, DK-2200 Copenhagen N, Denmark
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22
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Dalgaard JZ. Causes and consequences of ribonucleotide incorporation into nuclear DNA. Trends Genet 2012; 28:592-7. [PMID: 22951139 DOI: 10.1016/j.tig.2012.07.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Revised: 07/12/2012] [Accepted: 07/31/2012] [Indexed: 12/01/2022]
Abstract
Intuitively one would not expect that ribonucleotides are incorporated into nuclear DNA beyond their role in priming Okazaki fragments, nor that such incorporation would be functional. However, several recent studies have shown that not only are ribonucleotides present in the nuclear DNA, but that they can be incorporated by at least two different mechanisms: random 'mis'-incorporation of ribonucleotides, which occurs at a surprisingly high frequency; and site-specific incorporation at a stalled fork. Importantly, in the latter case, the ribonucleotides have been shown to have a biological function - acting to initiate a replication-coupled recombination event mediating a cell type change. Traditionally, it has been thought that 'random' ribonucleotide incorporation causes genetic instability, but new evidence suggests there may be a fine balance between mechanisms preventing and incorporating ribonucleotides into genomic DNA. Indeed, genomic ribonucleotides might have diverse roles affecting genetic stability, DNA damage repair, heterochromatin formation, cellular differentiation, and development.
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Affiliation(s)
- Jacob Z Dalgaard
- Division of Biomedical Cell Biology, Gibbet Hill Campus, University of Warwick, Coventry, CV4 7AL, UK.
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